corral
Correspondence Analysis for Single Cell Data
Bioconductor version: 3.23 · Package version: 1.22.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Correspondence analysis (CA) is a matrix factorization method, and is similar to principal components analysis (PCA). Whereas PCA is designed for application to continuous, approximately normally distributed data, CA is appropriate for non-negative, count-based data that are in the same additive scale. The corral package implements CA for dimensionality reduction of a single matrix of single-cell data, as well as a multi-table adaptation of CA that leverages data-optimized scaling to align data generated from different sequencing platforms by projecting into a shared latent space. corral utilizes sparse matrices and a fast implementation of SVD, and can be called directly on Bioconductor objects (e.g., SingleCellExperiment) for easy pipeline integration. The package also includes additional options, including variations of CA to address overdispersion in count data (e.g., Freeman-Tukey chi-squared residual), as well as the option to apply CA-style processing to continuous data (e.g., proteomic TOF intensities) with the Hellinger distance adaptation of CA.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("corral")Details
| Maintainer | Lauren Hsu <lrnshoe@gmail.com> |
| Author | Lauren Hsu [aut, cre] (ORCID: <https://orcid.org/0000-0002-6035-7381>), Aedin Culhane [aut] (ORCID: <https://orcid.org/0000-0002-1395-9734>) |
| License | GPL-2 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | BatchEffect, DimensionReduction, GeneExpression, Preprocessing, PrincipalComponent, Sequencing, SingleCell, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/corral/ |
Citation
From within R, enter citation("corral"):
Lauren Hsu, Aedin Culhane. corral: Correspondence Analysis for Single Cell Data. doi:10.18129/B9.bioc.corral, R package version 1.22.0, https://bioconductor.org/packages/corral.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Alignment & batch integration of single cell data with corralm
- Dimension reduction of single cell data with corral
Download
Follow the installation instructions to use this package in your R session.
| Source package | corral_1.22.0.tar.gz |
| Windows binary (x86_64) | corral_1.22.0.zip |
| macOS binary (arm64) | corral_1.22.0.tgz |
| macOS binary (x86_64) | corral_1.22.0.tgz |
Dependencies
Imports: ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix, methods, MultiAssayExperiment, pals, reshape2, SingleCellExperiment, SummarizedExperiment, transport
Suggests: ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat